Intersect Wars: Vendetta
by Grey Alchemist
Summary: Post-Season 2 AU. Shortly after uploading the Intersect 2.0, Chuck is taken by a CIA scientist. After thirty-two months in captivity, he regains his freedom. Now it's time for him to deal with the fallout of his imprisonment.
1. Release

_**Author's Note:**_ I used to be a big fan of the _WWE_, _WCW_, and _ECW_ back in the day. I'm not a fan of mma and I haven't watched _Raw_ or _SmackDown_ in years, but the idea for this story came out of the fascination I used to have with professional wrestling. I wasn't planning to do anything with this until later, but I've been having some thoughts about _Regenesis_ and while that was happening, I just went ahead with this. Hope you like it:

_**Here's this:**_ I don't own _Chuck_, otherwise, I would have smacked upside the head the moron who came up with this one really stupid idea for season 5 I read about a couple of days ago.

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Release

_December 20, 2011_

_7:00 pm_

"Ladies and Gentlemen! Welcome to _Intersect_ _Wars_ _XXXI!_" The resounding voice of the commentator continued, "We have got a great card planned for tonight!" The cheers and applause worthy of an arena could be heard loud and clear.

"Yes, we do," said the voice of his co-commentator. "We have for you tonight: A Team Battle undercard, which should be pretty interesting. Then, for the main event, we are proud to present our reigning champion _Carmichael!_" He paused as the cheering intensified at the mention of the name, "In a one-on-one match, against our newest challenger _Stryker!_" Again he paused, this time for the cacophony of booing that rang out. "Two men enter! One walks out!"

"Right, you are Stan. Well, he may not _walk out_ but we _will_ have a winner," said the voice of the first commentator. "Carmichael has won the last thirty consecutive matches, has been champion since _Intersect_ _Wars _began... could tonight be the night the streak finally comes to an end?"

"I don't know Mike; he does have a way of surprising us. I mean did you ever in your _life_ think that a guy that looked like him would win his _first_ match, let alone twenty-nine others?" The excitement typical of color commentary was in full swing.

"Yeah, that was certainly a surprise. I thought he was going to get ripped apart. But, as we now know: with the Intersect in play, anything can happen!"

"For those of you with us for the first time, let's take a look back at that match. Roll the tape..."

**-0-**

As the footage was streamed to the millions watching at home, the two commentators had a conversation between themselves.

"Hey, Mike?"

"Yeah?"

"Do you ever wish we actually had a live audience to play off of here? I mean this thing is a monster... as popular as it is, don't you think he'd jump at the chance to rake it in even more?"

"Seriously? Look at this set up, man," Mike said pointing to their surroundings. "We are in a re-enforced booth, far above a steel cage surrounded by green-screens. Do you honestly think he'd let anyone else near this place?"

"No, but I mean, why not take it out on the road? I don't know about you, but I'm tired of pushing these damned buttons and listening to canned cheering."

Mike let out a sigh. "Stan... listen to yourself," he offered.

"What?"

"Did you forget that they modulate our voices? That the audience only knows us through our avatars? C'mon man, don't be stupid. We are in a secluded bunker in the middle of nowhere. Do you think any of this is legal? I mean Carmichael alone has _killed_ five guys!"

"I know that!" Stan retorted, feeling less than pleased at the dig at his intelligence. "I wasn't talking about America or any of those places. Maybe Cuba, though."

"Just let it go and be happy we get paid as well as we do for doing this job. Do you know how many people would love to get their hands on the Intersect technology? The boss would never risk that."

"I'm just sayin'..."

"Well, don't. We're back in five, get ready."

**-0-**

"Well, there you have it folks. Was that something or what?" Mike was back to his on-air persona.

"I still can't believe it; and I was there!"

"Okay. It's time to get this show under way; coming up: the Team Match. Who do we have tonight, Stan?"

"Well, Mike, tonight we have Blue vs. White. The last time these two teams met, White lost a team member, so tonight will certainly be an interesting match up."

"There is definitely bad blood there. I can't wait," Mike said, full of anticipation.

"Let's take a look at the screen," Stan directed as different images began flashing on the monitors. Finally, they slowed down, until only one remained, "Our course tonight: The Arboreal!"

"There's a lot of hiding places among those trees, strategy will be key. This is bound to be a good one."

"The teams are taking their places. Here we go."

On the course, Mike's voice came over the loudspeaker, "White, ready! Blue, ready! In five! four! three! two! one! Go!"

"And, we're off folks. This match has officially begun. Mike, who's your money on?"

**-0-**

_December 20, 2011_

_7:30 pm_**  
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On the other side of the compound, a man approached a holding cell. "Okay, Chuck. It's about that time again. You ready?"

Chuck Bartowski sat on his cot with his head hanging low, ankles and wrists chained together. "Please, Smith. Don't make me do this. Just let me go... I don't even know where we are, you can disappear."

"Must we go through this every time, Chuck? I've already told you I'm not going to kill you. What more do you want? You know the deal: I will let you go when I get what I want." Sparing an appraising glance at Chuck, he continued, "Cheer up, Chuck! Because, guess what? Tonight is the night. I don't need you anymore. You win this match and you're free to go, how's that?"

"You already have me where you want me, no need to play games," growled out Chuck.

Smith reached into his pocket and pulled out a pair of sunglasses. "Who's playing games? I'm a man of my word."

As Smith opened the cell door and approached, Chuck asked, "What are you doing?"

"Why removing that pesky little extra bit of programming of course, unless... you want me to leave it?" He held back the glasses as he waited for Chuck to answer.

Chuck thought about the question for a moment. He knew he would be at a disadvantage if he put on the glasses, but if he was ever to get out of here, he couldn't risk the safety of those near him. Reluctantly, he looked up and leaned his head forward. Smith smiled and put the glasses on him. The images engaged in the lenses and thirty seconds later Chuck was free. He no longer had Smith's sick programming in him, but he still had the 2.0. He would make it.

"There, all better. Now all you have to do is make it through this match and you'll never see me again. Your fate is entirely in your hands, Chuck. I wish you luck, but I won't be holding my breath." He laughed mockingly at Chuck and started making his way out of the cell and down the hallway.

The anger rose in Chuck. Anger at being imprisoned, anger at what he had been forced to do, and anger at one Edward Smith. He screamed out, "Smith! I _am_ going to get out of here!" In a low voice he added, "And when I do, I will find you and I will make you pay."

Chuck decided to focus on his immediate problem. If his opponent was anything like the others, and he was sure he was, he would have to defend himself. Even after everything he'd been through, he was still Chuck Bartowski and it wasn't in his nature to hurt people but it seemed he wouldn't have a choice. He would try to end the match as quickly as he could. Knock his opponent out before things got out of control. If he couldn't, well, he would do what he had to do...

**-0-**

_December 20, 2011_

_7:50 pm  
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"Oh! And there goes Johnson! Blue is down to one active fighter! It comes down to this folks: a one-on-one battle to decide the winner."

"I can only imagine how tired these two must be, Mike. They have been exerting a lot of energy over the past half-hour; they can't have much left in the tank." Stan was subdued at this point, expecting the match to fizzle to conclusion.

"I agree, I don't think they're going to last much longer. I know some of you are going to be disappointed but, at this point, it looks like White won't be able to even the score this time around."

At that moment the last remaining member of Blue leapt out of a tree branch down onto the remaining member of White, driving them both down to the ground hard. White just managed to push Blue off before he could lock his choke hold and end the match. They both rolled and stood, staring each other down. Blue went on the offensive, intending to tackle White down. White sidestepped him and pushed Blue forward trying to ram him into the tree. Blue recovered and used his momentum to run a couple of steps up the tree, intending to back-flip off. White capitalized on the time it took to complete the flip. He raced to Blue, locked his arms around Blue's waist in mid-flip and suplexed him into the ground with all the force he could muster, breaking Blue's neck and ending the match.

White remained on the ground, breathing heavily, arms splayed, one leg stretched out, the other pulled in perpendicular to the ground.

"I spoke too soon!" Mike cried. "_Holy_ _crap_! Did you just see that! Stan, did you imagine anything like this happening?"

"Hell no, Mike! I thought these two were done! I thought choke-out for sure, this is _definitely_ better!" Stan said, matching Mike's enthusiasm.

"Ladies and Gentlemen, there you have it! That last-second move by Tremaine has ended the match. Blue will now have to get a replacement for Wells. Looks like White got even after all."

"That's why I love this sport, Mike: you can never be too sure what's going to happen," Stan added. "I think this is the perfect lead-in to our main event."

"Speaking of which, it is now time for our main event folks! I hope you're ready for a hell of a show."

"Let's go to our main arena, it's time to introduce our fighters."

"First up, standing at 6 foot 6, and weighing in at 220 pounds: Stryker!"

The camera switched to the arena entrance as the scowling, bald-headed mountain of muscle walked in and made his way to the cage. The referee, who was really more of a doorman, opened the cage door for Stryker.

**-0-**

Backstage, Chuck had been escorted to the entrance of the arena, where Dr. Smith was waiting for him.

He began to unlock Chuck's restraints. "Well, this is it, Chuck. Thanks for such a fruitful partnership," Smith said as he attached the electronic gauntlet-like device Chuck had become used to wearing on his forearm. "I suppose it would make me a bad sport to send you out there without this; ah well, gotta keep up appearances anyway. It's not like it'll help you much," he said as he finished the last latch. "Good luck, Bartowski, really. I think I may even shed a tear if you don't make it out, but then, I always was too sentimental."

Chuck said nothing but had a disgusted look on his face. He heard his name being called out over the arena speakers and was shoved through the entrance. "Bye Chuck!"

**-0-**

_December 20, 2011_

_8:00 pm_**  
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"And now," Stan started, "Our reigning champion, standing at 6 foot 4, and weighing in at 190 pounds: Carmichael!"

Chuck stumbled slightly after being shoved and made his way to the cage. He looked around at all the green surrounding him, hopefully this would be last time he saw this place and not because he had been killed during the match. He tried to focus his mind; he needed to be prepared to do whatever it took to make it through. He couldn't let Smith get away with what he'd made him do.

The referee opened the cage door for him, and as he stepped in, he took a look at his opponent for the first time.

Chuck's eyes bugged out. "Aw... fuck." _I'm fighting Bane!_ "Smith! I'll pay you back for this! I swear!"

Stryker grinned evilly at Chuck.

Mike interrupted the stare-down. "Now, let's see what today's style is," a double-sided screen set-up was lowered into the cage, images of different fighting styles began to cycle through, and then stopped abruptly.

Stan jumped in," Oh! And we have Muay Thai!"

Chuck and Stryker both looked at the illustration of a man elbowing his opponent across the face and flashed.

They both assumed fighting stances at the same time.

"Here we go folks, what you've all been waiting for; the main event is about to heat up," Mike commented.

Chuck knew he was at a disadvantage, he needed to end the fight as soon as possible or he would lose.

Stryker went on the attack sending a kick flying towards Chuck, he joined his knee and elbow to block. The impact sent him stumbling backward. _Damn, he almost broke my arm_, Chuck thought as he tried to rub the hurt away. He definitely needed to end this fast.

Stryker came at him with a punch, Chuck grabbed his wrist to deflect it and moved his head when Stryker's other fist shot out.

Chuck kicked Stryker in the gut and pushed him back, putting some distance between them.

"Stryker has wasted no time at all in this fight, he really wants to take Carmichael out," Stan spoke.

"Carmichael on the other hand seems to be struggling, not the fighter we're used to seeing out here," Mike added.

"Not at all Mike. Carmichael seems like an amateur more than a champion right now. What is going on?"

"I don't know Stan, but if he doesn't get back on his game fast, he's going to be in some serious trouble."

Chuck felt himself getting tired and knew he wouldn't last much longer against his more powerful opponent; if he was going to try something, he'd have to do it soon.

Just then, Stryker launched another vicious kick aimed at Chuck's left leg. Chuck raised his knee and blocked, at the same time, using his longer limbs, he sent an outstretched hand straight at Stryker's throat. His blow connected and left Stryker unable to breathe.

Stryker reigned in his hands in an effort to soothe his injured trachea. Chuck took advantage and quickly followed by sending a kick straight to Stryker's left side, knocking what little oxygen he had left out of his lungs.

Stryker clutched at his side and hunched over. Chuck went around him and immediately put him in choke hold; he wrapped his legs around Stryker's torso and held on as tightly as he could. This was it. This was the only chance he was sure to get. He had to end it now. If he couldn't, it would turn into a kill or be killed situation and that's something Chuck did not want.

"_Holy crap! _This one looks to be just about over!"

"Carmichael has surprised me again, Stan. I'll admit I was a little worried there that this would be the end of his incredible championship reign."

Stryker fell to the ground and Chuck could feel the fight leave him. After a few more seconds, he was out completely. Chuck kicked him on the side but got no reaction. He got out from underneath Stryker and saw his body lying motionless on the mat. Chuck looked for the referee to open the cage door for him but he had disappeared.

"Hey! I won, Smith!" Chuck yelled. "Let me out!"

The video stream had been severed. Stan and Mike were gone. The lights went out in the arena.

"What happened to the deal you bastard!" Chuck shouted as darkness replaced light.

Chuck looked around him when he heard gas being released from all sides of the cage. He quickly started to feel the effects.

He tried to hold on to consciousness as long as he could but it was a losing battle. He fell to his knees and started to wobble.

_I'll get you Smith_, was his last thought before he fell face first onto the mat.

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_**Author's Note:**_ I've now added dates to the first four chapters and will continure to do so from here on in. It should make events easier to place.

On another note: if you've read any of my other stories, you know I don't really do action. So, for reference for Chuck's fight, I watched a video titled: _Muay Thai Kick Boxing instruction with Bear Essential Combat_ from Daily Motion.


	2. Capture

_**Author's Note:**_ Thank you to those that reviewed chapter 1. I know what I said, but here's chapter 2 anyway:

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Capture

_April 27, 2009_

_9:37 pm_

For once in his life, John Casey was speechless. "Uh..." The geek had just taken out five armed opponents. They hadn't been able to land a single hit.

"Chuck?" Sarah was wide-eyed.

Chuck didn't know what was going on, he was in a daze. "Guys... I know kung fu." He quickly remembered the situation they were in. Sarah was looking at him like he was a stranger. Everything had changed. Bryce had told him she was going to stay and now—_Bryce!_ One of the Ring's agents had dragged his body away. Before anyone could say anything, he sprinted out of the room.

"Where are you going, moron?" Casey shouted after him.

"They have Bryce!" Chuck sped down the hallway. As he made a turn, he caught up with the agent that was dragging Bryce behind him, almost at the door.

He saw Chuck coming, let go of Bryce, and went to draw his gun. He aimed at Chuck and fired but he was too slow. Chuck flipped in the air, dodging the bullets. He landed in front of the agent. Chuck sent a powerful kick to the man's head that had him corkscrewing in the air before he hit the ground unconscious.

Casey stayed in the Intersect room securing the intruders. Sarah went after Chuck. She found him lifting Bryce's body from the floor.

"He deserves better," he said. "Where's Casey?"

"Securing the guys you knocked out," she said, uncertain of how to interact with Chuck. "He called for back-up. They should be here shortly."

He nodded and started to walk back towards Casey. Bryce was dead. The Intersect was back in his head; well, _an_ Intersect anyway, this one was a whole new beast. Sarah seemed distant. This was not how things were supposed to go. "Sarah—"

"Not now, Chuck," she said, keeping her eyes forward and dragging the unconscious body behind her by his foot.

"Fine, but we _will_ talk," he answered determinedly.

**-0-**

Fifteen minutes later back-up arrived. Casey stood pacing around the captured agents, making sure they couldn't get free. Sarah sat propped up against a wall, looking down at the ground, not wanting to make eye contact with Chuck. Chuck sat beside Bryce, looking down at his lifeless body, but not really focusing on it. Instead, he was dwelling on the span of their entire friendship, everything that had happened between them, and how things had ended. In the end, in spite of how he felt at times, he was genuinely sad over Bryce's death. True, he had hated him at one point, but he never wished for his death.

Two medics grabbed Bryce's body by the feet and shoulders, picked him up and loaded him on a gurney. Completely ignoring Chuck in the process.

He started to protest against the rough treatment of the body. "Hey, be—Agh!" he collapsed to the floor.

"Chuck! What's wrong? Are you hurt?" Sarah raced to him. Casey looked over his shoulder as he was handing over the prisoners.

"Every inch of my body feels like it's on fire," he groaned. "You know how you feel really sore after working out? Well, it's like that, only much worse," he offered. "But don't worry, I'm fine."

"Fine?" She questioned. "You can't even stand up!"

"Can too!" He argued and tried standing, only to groan loudly again and flop back down. "Okay, so maybe not right this second, but that's just because of my cramped muscles."

"Just don't move," she told him. "Casey, help me pick Chuck up. We need to get to Castle and call Beckman."

Casey walked over to Chuck, picked him up, threw him over his shoulder and started walking out. "What?" He asked at the look he got from Sarah. "Just like a sack of potatoes," he shrugged. "It's much easier this way."

"Hey! I'm right here," Chuck informed, his head halfway down Casey's back.

"Shut up, moron."

Sarah rolled her eyes and walked out.

**-0-**

_April 27, 2009_

_11:15 pm_**  
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Casey went to set Chuck down in one of the cots in Castle while Sarah connected with the General.

"Report, Agent Walker," Beckman began as soon as she appeared on screen.

"The situation seems to be under control for now. The back-up team you sent is cleaning up the facility now. We have the intruders in custody. They didn't get anything, Ma'am," Sarah finished.

"What about Bartowski, where is he?" She asked just as Casey was making his way into the room.

"I just put him down in one of the cells, Ma'am," answered Casey.

"Why? What's going on?"

"This new Intersect—the things it let him do—," began Sarah, "as far as I can tell, it put a strain on his body he's not used to and now he's suffering the effects. He's basically overexerted himself, but I don't know if there are any other effects from the new upload."

"This is a damned nightmare. I can't believe we're back to this," Beckman sighed heavily. "This is Doctor Edward Smith." A photo of a slightly graying man in his mid-forties appeared on the screen beside Beckman. "He should be arriving at Castle shortly. He was going to perform a full work up on Larkin after the upload, but given the turn of events he will now be working on Chuck instead. He knows everything about the Intersect project; he actually helped write some of the new programming. Help him with whatever he needs. We have no idea who attacked us tonight. We need Bartowski back on his feet." She was about ready to end the conference. "Keep me updated."

"Excuse me, General?"

"Yes, Agent Walker?"

"What about Agent Larkin? What's going to happen to his body?" She had made a promise to Bryce and the least she could do after rejecting him was to keep it.

"We're taking care of everything. That's all you need to know."

"But—" Before she could go on, the screen went dark.

"Still stuck on Larkin, I see." Casey said beside her. "I feel sorry for the geek. You really did a number on him."

"Shut up, Casey," she snapped. She wasn't in the mood to deal with him. "You know what? Why don't you go look for Chuck's dad? We might need his help with Chuck."

He grunted annoyed. "Fine, I'm going, only because if anyone can help here, it's Orion," he said as he headed up the stairs. He was mumbling along the way, "Damn CIA, can't keep it in their pants..."

**-0-**

_April 28, 2009_

_12:20 am_**  
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"Hey! You guys didn't forget about me did you!" Chuck was on his back on the cot. He hadn't moved so the soreness was minimal.

Sarah didn't want to talk to Chuck right now, but she was the only one there. She sighed and went to check on him.

"You okay?"

"Hey, there you are," he said brightly.

"What do you need?" Sarah asked shortly.

"Can we talk for a minute?" He said, shifting his head to get a good look at her.

"I'm a little busy right now, Chuck." she said.

"Come on, Sarah, we need to talk," he pleaded.

"There's nothing to talk about, not anymore." She turned to leave.

Chuck called on every bit of strength he had and got himself into a standing position.

Sarah saw him stumble and rushed to keep him upright. They got tangled up and fell back towards the cot. She ended up with Chuck on top of her, looking down straight into her eyes. "Chuck," she strained, "you're kind of crushing me here."

"Oh, sorry." Chuck struggled to hold himself up on his elbows but didn't move off of her.

"Um... I was thinking more along the lines of you getting off me so I can stand up," she said.

"Sorry, Sarah, but I told you: we're going to talk."

"Chuck," she warned, "I don't have time for this. Move or I'll mohmmm—"

She didn't get to finish, as Chuck brought her into a kiss, the likes of which she hadn't experienced since the time Roan tried to teach him the art of seduction. He finished with a small peck on her lips. They were both actively trying to catch their breath. He brought a hand up and caressed her cheek. "Bryce told me you weren't leaving, Sarah." Sarah was still too taken by the kiss to properly answer. "You were going to stay, weren't you? With me?"

"It doesn't matter anymore," she said softly. "Nothing's changed."

"It _does_ matter. Everything's changed. You chose _me_," he said holding her gaze. "I'm not just going to let that go. Not anymore. After seeing Bryce die right in front of me, I'm not willing to not go after what I want. Life's too short."

"Chuck, please. I'm still your handler, you're still my asset, we can't," she said resignedly. "You were out. Why did you have to go and upload the new Intersect?" She said, her voice almost breaking.

"I did it because of you; you told me I was _that_ guy. You made me want to be better, to live up to your view of me. How could I not?" He continued before she could say anything, "More importantly, you _needed_ me to be that guy tonight. If I hadn't uploaded the new Intersect, they would've killed you, Sarah. It allowed me to save you and I will always do whatever I have to, to keep you safe." His tone left no room for doubt. "I know I've complicated things, and you're mad at me right now, but I don't regret what I did. I would do it all over again if it meant keeping you safe."

The intensity in Chuck's eyes left Sarah at a loss for words. "Chuck—"

Chuck stopped her to lighten the mood "Plus, I think I can take you and Casey now," he said smiling.

Sarah was surprised by the change in direction but realized what Chuck was doing for her. "Oh? You're a little full of yourself aren't you?"

"Well... I mean, I did just take out six guys... by myself... unarmed." He waggled his eyebrows.

Sarah chuckled. "Yeah and now you can barely move." She poked him in the arm.

"Sore! Sore! No poking there...or anywhere else." He squeaked out, much to her delight. He kissed her again, more subdued this time. "Seriously, Sarah, I meant what I said. I'm not just going to let you go this time. I'm going to fight for us. Can I count on you—"

Before he could finish, a voice called out from the other room. "Hello? Agent Walker? Colonel Casey?"

"Who's that?" Chuck asked as he moved off of Sarah.

"Must be the doctor Beckman sent to check you out," she reached for one of her knives. "Just in case, stay here," she said and went to check out the intruder. She made her way to the conference room and immediately recognized the man Beckman had identified as Dr. Smith. "Doctor Smith," she spoke up.

"Agent Walker, I presume?" Sarah nodded. "Where's Colonel Casey? I was told he'd be here."

"He's not here at the moment; had something to check out."

"I see," he said as a small smile came to his face. "Would you mind showing me to my patient, then?"

Sarah had an uneasy feeling about this man. "This way," she said, keeping her distance.

They arrived back at the cell where Chuck was resting. "Chuck, this is Doctor Edward Smith," she said making sure to emphasize his full name, "he's here to check you over, make sure you're okay." She watched as Chuck looked at the man but saw no signs of a flash, still, she felt there was something off.

"Hello, Mr. Bartowski," began Smith. "I must say, you're not the patient I was expecting, but I've read your file. In my opinion you are a better candidate than Agent Larkin anyway."

Chuck shot a questioning look at Sarah; there was something weird about this doctor's demeanor.

He pulled out a syringe with a clear fluid inside.

Sarah wrapped her hand around his wrist, restraining it. "What's that?"

"Relax, Agent," he said smiling, too broadly she felt. "It's just something to help him with the muscle pain. General Beckman filled me in on the side effect he's going through." Sarah let go and he injected Chuck in the arm.

Chuck began to feel the effects almost immediately.

"Can you help me sit him up?" He asked Sarah as he moved to put the syringe in his coat pocket.

Sarah bent down and grabbed Chuck by the arm. Chuck felt himself get drowsy but the pain wasn't going away. He was fast loosing the ability to stay awake. "Sarah! he—" Smith's hand shot out with a can aimed at Sarah. He pressed the nozzle and a cloud of gas engulfed her face. She managed to knock the can out of his hand but she had already inhaled the gas. This one worked quicker than the injection and she immediately lost the ability to keep herself up.

"He drugged me? He's a bad man? Words hurt, Chuck," Smith said as he straightened himself up. "You know, no one appreciates a true genius; always Orion this, and Orion that. What's so special about him?" he was talking mostly to himself.

"Chuck..." Sarah said, fighting to keep awake.

Chuck tried to move toward Sarah to no avail. "Sarah... I love you..." That was the last thing she heard before she lost consciousness.

"Oh!... isn't that sweet! You two?" Smith said as he pointed between Chuck and Sarah. "Well, now I kinda wish it had been Larkin. Oh well, I think it's time for us to go. Don't want to be around when Colonel Casey gets here."

Chuck tried to hold on but, he too, succumbed to the drug's effects. The last thing he saw was Sarah crumpled on the floor.

* * *

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_**Author's Note:**_ So, if you read the summary for this story when I first posted chapter 1, you can forget about it. It does apply to the first part, but then the story goes in a different direction I just thought of while writing this chapter.


	3. Found

_**Author's Note: **_I had some blockage lately; this is my attempt to get back into a writing mindset, so it might be a little... off. Here goes chapter 3:

* * *

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Found

_December 21, 2011_

_6:43 am_

It was hard to think. A muffled voice started to fight its way through the haze.

"Chuck... come on, Chuck, wake up," it beckoned. It was a soft, soothing voice. There was something familiar about it, something comforting.

Chuck fought to do as the voice asked. It was hard at first but made easier with each subsequent movement of his head. His head was aching; his eyes still shut, then—"Ow!" A stinging pain spread from the side of his face, his eyes shot open, only to close shut again from the onslaught of light attacking his corneas. The lights had been turned on again.

In the background he thought he heard, "Damn it, Casey! What the hell was that?"

**-0-**

"It worked, didn't it?" The Colonel shrugged.

Chuck chose that moment to slowly blink his eyes open again. He appeared to still be lying on the floor of the cage. Knelt on his right was Sarah, she was the most beautiful sight ever to fall before his eyes. A big, lazy smile formed on his face. He started wondering if he was hallucinating, then his gaze shifted behind Sarah, slowly making its way upward. "Ah!" Chuck yelled. "Not pretty!"

Casey added a growl to the scowl already on his face. "Thanks a lot, moron."

"Chuck." Sarah launched herself and pinned him to the ground. She wrapped her arms around him and held on for dear life: he wasn't complaining. He smiled wide as he looked up at Casey. He'd desperately missed his friends and family, even Casey.

"Ugh... You two make me sick," he said.

"Nice to see you too, Casey," Chuck replied as he returned Sarah's embrace.

Casey was glad to finally see his partner in person again, not that he was going to tell him that. "Whatever, we don't have all day. Get your asses up and moving."

"Sarah?" He asked softly.

"They can wait," she responded, not letting go.

"I couldn't agree more," he said, as he stroked her hair gently, "but as much as I like this, I've been lying here for—" He actually didn't know how long it'd been.

"A little over ten hours," Casey offered.

"Ten hours?" Casey nodded. "Well, anyway, I kinda need to stretch here... and maybe you guys can give me something for this stupid headache?"

Sarah loosened her hold and looked into his eyes. "Are you okay?" The concern was clear. "That's a stupid question. Of course you're not okay."

"Sarah, I get it," he said trying to calm her. "Yes, besides the headache, I'm okay."

"Walker, come on. You know we can't be wasting time here," Casey sternly reminded her.

Chuck looked between both of them, wondering what they were talking about.

Sarah got up and offered her hand. "It's okay, Chuck. We'll tell you all about it later."

Chuck took her hand and pulled himself up. Once he was upright, however, Sarah held on to his hand with a death grip. He looked down at their joined hands.

"What?"

"Nothing, nothing," Chuck looked over to where Stryker had lain. "Hey, guys, what happened to the guy I knocked out?"

"Taken care of," was all he got from Casey.

Sarah wrapped her free arm around his as they started to walk side by side.

"Not that I don't appreciate you guys being here but I had kinda given up on anyone coming for me. How did you find me? Actually, _where_ did you find me?"

"You don't know where you are?" Sarah spoke up.

"No. One minute I was in the Castle cell," he said, glancing over at Sarah before continuing, "the next I wake up chained in a cell in this place," Chuck pointed with his head to their surroundings. "I'm not even really sure how long I've been here." Chuck quickly took notice of Casey's questioning eyebrow. "Well, I didn't exactly have a TV or clock in my cell; and it's not like I have a watch," he said, holding out his wrists.

Casey took notice of the metal gauntlet on Chuck's left forearm. "Oh yeah, take that stupid thing off, Bartowski. We all know that's not the Intersect."

"Sorry, Casey, I can't do that. I need this thing," Chuck started to explain before Casey could turn his growling into words. "You're right, this isn't the Intersect, but without it I'll die." Casey's face showed surprise, as subtle as it was.

Sarah tightened her grip on Chuck as she looked straight at him. "What do you mean you'll die?"

"Apparently, it doesn't matter how high a retention rate someone has, the Intersect will kill them just the same." He looked to both Casey and Sarah and went on. "The higher your retention rate, the slower you'll be affected; but eventually, even someone with a one-hundred percent rate will be driven insane by the Intersect. From what Smith told me, your brain slowly fries and then you die." Chuck gently removed his left arm from Sarah's grasp and tapped the metal contraption. "This," he said, "keeps the Intersect in check. It regulates its activity and prevents it from overwhelming my neural pathways. Without it, it's only a matter of time before the Intersect gets to be too much for me to handle."

Casey and Sarah shared a knowing look before Casey spoke up. "How do you know Smith wasn't just pulling your leg? The way his fighters were dying, it seems like a waste of time to hook you all up with these things."

"Actually, mine is the only functioning one, the others were just for show, but I'll tell you about that later. You didn't answer my question. Where am I?" He was on alert, he'd seen the look that had been shared; after everything he had been through, he knew he could look after himself if they tried something. Chuck hoped they wouldn't.

"You're in Arizona. In the middle of the Grand Canyon, to be more precise," Sarah answered.

"One state over?" Chuck asked in surprise. "All this time I was that close to home?" Disbelief laced his voice.

"Two years, eight months, that's how long it's been; and yes, as far as we can tell you've been here the whole time. But Chuck, we looked everywhere, we tried everything, we just had no idea. Smith is a lot smarter than anyone thought. Even your father couldn't find this place."

Chuck turned his focus on Sarah, "My father? He's working with you?" That didn't sound like something Stephen Bartowski would do.

"Not exactly."

"Look, Bartowski, we don't have time for this." Casey interrupted. "We need to get out of here and report back to Beckman."

"Please, Chuck. I promise we'll answer all your questions but we need to go," Sarah said, once again taking his hand as she started to walk.

They made their way through a maze of hallways that were unfamiliar to Chuck, until they reached one with a bright opening at the end. _Sunlight_, Chuck squeezed Sarah's hand. It had been so long since he had been outside.

**-0-**

As they crossed the threshold, Chuck took in his surroundings. His eyes widened. "Wow," he breathed out. "This is where I've been all this time? It's so beautiful." They were standing amid a massive rock formation, a layer of green shrubbery covering a good amount of the red rock face.

Sarah smiled at Chuck's reaction.

"Yeah, like that's what's important here," Casey grumbled.

Before anyone else could say anything, Casey's radio crackled to life. "Colonel Casey?"

"Yeah?"

"Everything's been wiped clean in the control room, we couldn't recover anything."

"Is that all?" Casey was irritated by Smith managing to get away without leaving a trace.

"No sir. We also found several large rooms. They're simulations of various environments. We're pretty sure these are the rooms Smith used for his fights. We found the last one he used. There's still a dead body in here, sir."

"Have you searched the entire facility?"

"Yes, sir. All the cells were empty."

"Get to the helicopter, we've got what we came for, we're leaving."

"Yes, sir."

Casey turned to Chuck, who, for the first time had noticed the two helicopters to his right. "Smith is one devious son of a bitch. He carved out an entire complex in there," Casey said, pointing back inside. "No wonder we couldn't find you. Our equipment can't get through this much rock."

"So, what changed? How did you find me now?" Chuck asked as they made their way to one of the helicopters.

"We were trying to trace the location from the last fight, then the video feed cut out but we started to get a signal. We tracked it and it gave us this location," Sarah spoke up. "We didn't know if it was real or not but it was the first lead we've had, so we hopped on a plane, then into these two helicopters and made our way up here."

"Yeah, and then we found _you_, Sleeping Beauty," Casey interrupted. "Now, get your ass in here and take a seat. Anymore questions you have will have to wait until we get back to General Beckman. Apparently your scrawny behind is good for something after all."

Chuck scrunched his brow and turned to Sarah, who was seated next to him, "What's he talking about?"

"Chuck..." Sarah started, uncertain of how much to say, "There's—you've been gone a long time. Some things have happened. We need your help now more than ever." Sarah stopped him before he could ask anything. "Not now. I know you have questions but they'll have to wait."

"Colonel Casey, we're coming out now," came a voice from the radio.

"Good. Once everyone's out, seal the place." Casey turned to the pilot. "Take us back to the airport." The pilot nodded.

They were a couple of hundred feet up before the second helicopter lifted off. Chuck was looking out the window at the scenery below. He was taking the time to enjoy the moment because he knew once he was back in the fold things would get messy and complicated again.

He turned to Sarah and leaned in close to her ear. "Sarah, I know it's almost three years late, but can we please finish our talk later?"

"Sure, Chuck," she said, as she leaned over and kissed him. She rested her head on his shoulder and closed her eyes, his hand held firm in hers.

Chuck was taken aback, his eyes wide in surprise.

"Hey Romeo!" Casey called from the front. "You might want to close that mouth of yours!"

* * *

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_**Author's Note:**_ If you want to take a look at what Chuck was describing, look up: **File:Bighorn,_Grand_Canyon ** on Wikipedia. It's much better than I described.


	4. The Beginning

_**Author's Note:**_ Sorry to jinxed97 and the few of you that read this story, I know I said this chapter would be up last Monday but it just didn't work out. It was a long and tiring week. Just like I thought, but the good news is that I have my finalized schedule so things should be smoother. The bad news is that it's just like I thought, I have a lot to do and it doesn't leave much in the way of creativity for writing. If you haven't yet, you should really check out _Written in the Stars._ It's a damn good story and it got my imagination flowing again, hence this chapter. I hope you enjoy:

* * *

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The Beginning

_April 28, 2009_

_11:30 am_

"Hey, Chuck, wake up."

Chuck stirred slightly. He heard a voice calling to him but for some reason he was having trouble concentrating on what it was saying. He let out a low moan, signaling he was coming to. After a few moments he started to move more deliberately and felt strangely encumbered. He blinked his eyes open and shook his head to clear out the haze. The first thing he noticed was that his head was throbbing. The second thing he noticed was that he was lying down on something and he was sore all over, he couldn't fathom why that would be the case. The last thing he noticed, as he looked down his body, was that his hands were chained together, along with his feet. He blinked at what he saw, tilting his head in confusion, then quickly he started to panic. He didn't know where he was, who had him, how he got there, or what they would do to him. The only thing he could think of was that he had to try to get free and get away. He pulled his hands apart and kicked his feet out any way he could, but all that did was exacerbate the soreness he was feeling.

"Calm down, Chuck," spoke the voice again. "Don't hurt yourself."

Chuck stopped his movements and shifted his head to the left where the voice was coming from. It landed on a man who, for some reason, looked familiar to him. Then it hit him, he started to remember everything: Bryce, the download, the Ring, the Castle cell... Sarah. Then he remembered why this man looked so familiar: Doctor Smith.

"Ah, there we go..." He saw recognition in Chuck's eyes. He pulled a chair into the cell and moved to sit in front of the bed where Chuck could see him easier. "Welcome back, Chuck," he said smiling.

"Where's Sarah?" It was the first thing he thought to ask, his eyes narrow.

"Back where I left her, I suppose," he shrugged. "I'm guessing Colonel Casey's found her by now. Who knows, though?"

"You'd better not have hurt her," Chuck growled.

"Or what? You're really in no position to be making threats, Chuck," Smith said as he nodded towards his chains.

Chuck knew that, for the moment, Smith was right. "You're supposed to work for the CIA. Why are you doing this?"

"Why not?" He simply countered.

That angered Chuck. "You kidnapped me! You drugged an agent! That's all you have to say?"

"It's as good an answer as any," Smith delivered nonchalantly. "Don't take it personally. It really had nothing to do with you."

"Bryce." Chuck remembered what Smith had said back in Castle. "You're not part of Fulcrum or the Ring. I didn't flash on you. Why are you doing this?"

Smith ignored the question. "Okay, so I had to modify my plans a little. I mean, yeah, I was counting on Agent Larkin being delivered right to me instead of having to go after _you_, and I hadn't planned on taking out two agents but... I think things worked out just fine," he said, affirming his statement with a shake of his index finger.

"Hey!" Chuck did not like being ignored. "I asked you a question!"

"Hmm?" Smith looked back up at Chuck. "Right, what was that again?" He said, eyebrows raised inquiringly.

"Why are you doing this?" Chuck repeated. "You have to know General Beckman will—"

"She can do whatever the hell she wants," Smith interrupted harshly. His eyes narrowed. "It won't make a difference; no one's going to magically show up and rescue you. You are not going anywhere until _I_ feel like it."

Chuck was taken aback by the sudden change in demeanor. This version of Smith seemed like a man in complete control of his faculties, dangerous and fearsome.

In the blink of an eye, he was back to the aloof, if a bit crazed, disposition he'd had before. "Imagine a brilliant, handsome scientist toiling away on the greatest invention of the last thirty years," he began. "Making breakthroughs left and right, improving the technology in ways no one else could," he said. "Now, for all that effort and genius, do you know what he gets in return?" He eyed Chuck questioningly.

Chuck had nothing to say, he figured that wouldn't stop Smith from continuing. He was right. "Nothing... less than nothing," Smith answered his own question. "Because, while _I'm_ shining brighter than the sun, they're too busy looking for that second-rate amateur _Orion_ to notice me," he said bitterly.

"Hey!" Chuck protested. That was his dad after all and the man was no amateur.

"What? Trying to defend daddy?" Smith smirked. "After what he did to you and your sister? That's touching." He held a hand to his chest. "But, let me tell you a little something about Stephen Bartowski, Chucky boy: he's an unscrupulous, remorseless murderer," he said, smiling happily.

"Liar!" Chuck struggled against his chains trying to reach Smith.

"Oh," Smith said, frowning, "you hurt me, Chuck. I wouldn't lie to you." he shifted in his seat and leaned forward toward Chuck. "You see, that computer you happen to have in that head of yours?" He tapped Chuck's forehead with his index finger. "Well... it kills its host." Chuck's eyes went wide. "Not immediately, mind you. First, it will drive you insane... _then_ you die," he said leaning back in his chair. "And your father knew that." He corrected himself, "Well, he knew that about the original Intersect, with the modifications I've made to the new one, it'll happen much faster." He shrugged." Regardless, why do you think he wanted that thing out of your head so badly? He knew what would happen and didn't want it to happen to _you_."

Chuck was in shock. He didn't know what to say.

"It seems though, he had no problem with it happening to Bryce Larkin," he continued. "He happily modified the cube for the CIA to use. He didn't tell them anything at all about what would happen to Larkin. He sent him to his death without batting an eye; now, do you really think you know your father?"

"You're lying; my dad would never do anything like that!" Chuck protested.

"Next time you see him, ask," Smith shrugged. "And, don't let him give you the run-around. See how he reacts."

Chuck couldn't believe what he'd just heard. Smith seemed so sure. Could his dad really have known all of this? "So... I'm going to die?" He finally decided he needed to shift the conversion to something else.

"Well... yes," Smith responded. "At some point, I guess we all will. But it won't be from the Intersect," he added. "See, I'm much more benevolent than your father, plus, I need you alive so I've come up with a little something to counter the effects of the Intersect," he offered proudly.

"What do you want from me?"

"Nothing much. It's very simple really," he said as he began to stand. "I was woefully undercompensated for all my work at the CIA, so I've decided to take my work and get the compensation I deserve," he explained. "All I want from you is for you to be your wonderful Intersected self for as long as it takes... then you'll be free to go," he added as an afterthought.

"You mean you'll _kill_ me? I'm not going to do anything for you," Chuck assured.

"I'm kind of hungry," Smith said as he picked up the chair, completely dismissing Chuck's protest. "Yeah... I think I'm going to go get some lunch." He walked out of the cell and slammed it shut, leaving a confused Chuck behind. A moment later Smith's voice came from behind Chuck, "Where are my manners?" He asked apologetically. "I'll get something for you, too." Then he was gone.

**-0-**

_April 28, 2009_

_2:07 am_**  
><strong>

Sarah woke up in a Castle cell. She was lying on the cot Chuck had occupied earlier. She was momentarily disoriented before she swung her legs over the side and sat up. She forced herself into lucidity and everything started coming back. She remembered falling to the floor and wondered how she ended up on the cot. Then, she heard Casey's voice echoing through the halls, he was speaking with someone and sounded agitated. She got up and made her way towards his voice.

"He was long gone by the time I got here," Casey said. "He had an hour's head start and I couldn't go after him without leaving Walker unprotected," he finished. "Whoever vetted this traitor should be shot," he growled. He'd seen the surveillance footage of Smith drugging Sarah and Chuck. He'd also shown it to Beckman, although he'd left out the earlier part of the video that showed Chuck and Sarah in the cell. He figured it wasn't any of her business and it wasn't relevant to the current situation.

"I agree," replied a clearly angry Beckman. "Unfortunately, that was Graham," she lamented.

Casey grunted in agreement. Beckman's eyes flicked over his shoulder. He turned to find Walker standing behind him. "Walker, how you feeling?"

"Where's Chuck?" She answered.

"Gone," Casey told her.

"What are we doing to get him back?" She pressed.

"Agent Walker," Beckman spoke. Sarah shifted her gaze. "Edward Smith is an incredibly smart man," she informed. "He has covered his tracks well." She let out a deep breath and continued. "We need Orion's help. Colonel Casey's already informed me he's gone, but I can't imagine he'd leave his daughter without a way to contact him," she said. "Go to her; tell her whatever you need to but get her to contact Orion. Tell him his son is in danger," she instructed.

"Yes ma'am," Sarah responded.

"Contact me as soon as you have anything." The screen went black.

**-0-**

Beckman sat back in her chair after ending the conference with Casey and Sarah. Everything about the entire affair had been going wrong from the start; she was ready to pull her hair out. There would be a lot of explaining to do for her in the near future; she really needed some good news. She huffed out in frustration, took a composing breath, and reached for the phone on her desk. She dialed and waited for an answer.

"Yes, General?" came the answer on the other end.

"Doctor Ross," she started quickly, "we have to move up our timetable."

"By how much?"

"Is the backup ready?" she asked.

"Yes, ma'am," Ross answered. "We finished it yesterday."

"Good." Beckman continued, "What about your guest?"

"Back and stable," he answered, "though he won't be awake for at least several hours."

"Even better," she said, a tiny smirk of relief marking her features. Maybe she could still salvage the situation. "At least Fulcrum was good for something. Can you wake him up?"

"Yes, ma'am," Doctor Ross responded. "If we have to, although I'd prefer if he woke up on his own," the doctor informed her.

"Unfortunately, we don't have the luxury of time," Beckman answered. "Get the Intersect loaded and ready for upload, doctor," she instructed. "It's time for Agent Larkin to finish what he started."

"Yes ma'am."

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_**Author's Note:**_ I'm working on the next chapter of Regenesis, but don't know exactly when it'll be up. Maybe sometime during the week, but I have six reading assignments, four quizzes, and one speech to work on, so...


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